Your code doesn't work if the cleartext is not an exact multiple of 16 bytes in length (and maybe even if it is), because Crypt::Rijndael doesn't handle padding. Crypt::CBC handles that.

Your Perl code manually prepends/extracts the IV to/from the encrypted text. Crypt::CBC handles that.

Crypt::CBC has other features too, such as generating a random IV when so desired.

That's why Crypt::Rijndael should be in conjunction with Crypt::CBC instead of using Crypt::Rijndael's CBC mode.

The fix (and simplification) is:

use strict;
use warnings;
use MIME::Base64;
use Crypt::CBC;
my $key = pack("H*", "01020304050607080910111213141516");
my $cipher = Crypt::CBC->new(-cipher => 'Rijndael');
my $in = decode_base64(<>);
print "out = '", 
  unpack("N/A", $cipher->decrypt($in)), 
  "'\n";
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By the way, I removed use bytes since it was useless since you didn't use any numbers except the constants 0 and 16.

Also, I don't think Crypt::Rijndael's new sets $! (or ever returns false).

(Untested. I don't have these modules.)